CressInt: A user-friendly web resource for genome-scale exploration of gene regulation in Arabidopsis thaliana

Current Plant Biology

Volumn 3-4, Issue , 2015, Pages 48-55

  Chen, Xiaoting ^a,b   Ernst, Kevin ^a,b   Soman, Frances ^a   Borowczak, Mike ^a,b,c   Weirauch, Matthew T ^b  

^a University of Cincinnati   (United States)

^b UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

^c Erebus Labs   (United States)

Author keywords

Arabidopsis; Computational tools; Functional genomics; Gene regulation; Systems biology; Transcription factors; Web server

Indexed keywords

EID: 84949217254     PISSN: None     EISSN: 22146628     Source Type: Journal    
DOI: 10.1016/j.cpb.2015.09.001     Document Type: Article

References (37)

1. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408(6814):796-815.
2. de Lucas M., Provart N.J., Brady S.M. Bioinformatic tools in Arabidopsis research. Methods Mol. Biol. 2014, 1062:97-136.
3. Bassel G.W., et al. Systems analysis of plant functional: transcriptional, physical interaction, and metabolic networks. Plant Cell 2012, 24(10):3859-3875.
4. Brady S.M., Provart N.J. Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell 2009, 21(4):1034-1051.
5. Atwell S., et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 2010, 465(7298):627-631.
6. Gan X., et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 2011, 477(7365):419-423.
7. Sullivan A.M., et al. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Rep. 2014, 8(September 25 (6)):2015-2030.
8. Weirauch M.T., et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 2014, 158(6):1431-1443.
9. Kent W.J., et al. The human genome browser at UCSC. Genome Res. 2002, 12(6):996-1006.
10. Kersey P.J., et al. Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 2014, 42(Database issue):D546-52.
11. Berger M.F., et al. Compact: universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol. 2006, 24(11):1429-1435.
12. Barrett T., et al. NCBI GEO. Archive for functional genomics data sets-10 years on. Nucleic Acids Res. 2011, 39(Database issue):D1005-D1010.
13. Heinz S., et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 2010, 38(4):576-589.
14. Kottyan L.C., et al. The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. Hum. Mol. Genet. 2015, 24(2):582-596.
15. Berger M.F., et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 2008, 133(7):1266-1276.
16. Quinlan A.R., Hall I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26(6):841-842.
17. Franco-Zorrilla J.M., et al. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc. Natl. Acad. Sci. U. S. A. 2014, 111(6):2367-2372.
18. Boyle A.P., et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 2008, 132(2):311-322.
19. Kaufmann K., Melzer R., Theissen G. MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants. Gene 2005, 347(2):183-198.
20. Huang K., et al. Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors. EMBO J. 2000, 19(11):2615-2628.
21. Oh E., et al. PIL5: a phytochrome-interacting bHLH protein, regulates gibberellin responsiveness by binding directly to the GAI and RGA promoters in Arabidopsis seeds. Plant Cell 2007, 19(4):1192-1208.
22. Bu Q., et al. Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis. Plant Mol. Biol. 2011, 77(4-5):501-511.
23. Crooks G.E., et al. WebLogo: a sequence logo generator. Genome Res. 2004, 14(6):1188-1190.
24. Chica C., et al. Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation. Front. Life Sci. 2013, 7(1-2):80-87.
25. Willing E.-V., et al. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nat. Plants 2015, 1:14023.
26. ÓMaoiléidigh D.S., et al. Control of reproductive floral organ identity specification in Arabidopsis by the C function regulator AGAMOUS. Plant Cell 2013, 25(7):2482-2503.
27. Pajoro A., et al. Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol. 2014, 15(3):R41.
28. Wuest S.E., et al. Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA. Proc. Natl. Acad. Sci. U. S. A. 2012, 109(33):13452-13457.
29. Oh E., et al. Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. Elife 2014, (May 27):3.
30. Heyman J., et al. ERF115 controls root quiescent center cell division and stem cell replenishment. Science 2013, 342(6160):860-863.
31. Fan M., et al. The bHLH transcription factor HBI1 mediates the trade-off between growth and pathogen-associated molecular pattern-triggered immunity in Arabidopsis. Plant Cell 2014, 26(2):828-841.
32. Zhiponova M.K., et al. Helix-loop-helix/basic helix-loop-helix transcription factor network represses cell elongation in Arabidopsis through an apparent incoherent feed-forward loop. Proc. Natl. Acad. Sci. U. S. A. 2014, 111(7):2824-2829.
33. Moyroud E., et al. Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor. Plant Cell 2011, 23(4):1293-1306.
34. Pfeiffer A., et al. Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis. Mol. Plant 2014, 7(11):1598-1618.
35. Zhang Y., et al. A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis. PLoS Genet. 2013, 9(1):e003244.
36. Brandt R., et al. Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses. Plant J. 2012, 72(1):31-42.
37. Huang W., et al. Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 2012, 336(6077):75-79.